Sorry for the confusion. I use only one DA parallel layout for my problem in spite of the fact that I use MAC-staggered grid (I added one extra cell to the end of the domain in each direction so that I overcome the difficulty of one extra cell associated with each velocity in the corresponding direction, i.e. one extra u-grid exists in x-direction or one extra v-grid exists in y-direction). So, the vectors (global and locals) are derived from same DA but they do not refer to the same physical location. I could fix this if I create DA for each velocity and scalar components and set the coordinates for each of them separately, but I would rather not do this at this point.
I hope I was clear. Best, Mohamad On Thu, Jan 19, 2012 at 3:20 PM, Matthew Knepley <knepley at gmail.com> wrote: > On Thu, Jan 19, 2012 at 5:19 PM, Mohamad M. Nasr-Azadani <mmnasr at gmail.com > > wrote: > >> Thanks Mat, >> Use the DA coordinate mechanism and you can get the coordinates as a >> parallel Vec. >> >> well, that won't be working for me since although I use one DA and the >> parallel vectors derived from same DA, yet I am using staggered grid >> formulation. So, there the coordinates could be different for different >> vectors. >> Is there any other way around this ? >> > > I do not understand what you mean, be more specific. > > Matt > > >> On Thu, Jan 19, 2012 at 6:59 AM, Matthew Knepley <knepley at gmail.com>wrote: >> >>> On Thu, Jan 19, 2012 at 2:50 AM, Mohamad M. Nasr-Azadani < >>> mmnasr at gmail.com> wrote: >>> >>>> Hi guys, >>>> >>>> I have compiled petsc to use HDF5 package. >>>> >>>> I like to store the data from a parallel vector(s) (obtained from >>>> structured DA in 3 dimensions) to file using VecView() in conjunction with >>>> PetscViewerHDF5Open(). >>>> >>>> I followed the example here >>>> http://www.mcs.anl.gov/petsc/petsc-current/src/dm/examples/tutorials/ex10.c.html >>>> and everything looks fine. >>>> >>>> However, I had a couple questions: >>>> >>>> 1- When I am done writing the parallel vector obtained from the DA (and >>>> PETSC_COMM_WORLD), >>>> >>>> // Create the HDF5 viewer >>>> PetscViewerHDF5Open<http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Viewer/PetscViewerHDF5Open.html#PetscViewerHDF5Open> >>>> (PETSC_COMM_WORLD<http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Sys/PETSC_COMM_WORLD.html#PETSC_COMM_WORLD> >>>> ,"gauss.h5",FILE_MODE_WRITE,&H5viewer); >>>> // Write the H5 file >>>> >>>> VecView<http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Vec/VecView.html#VecView> >>>> (gauss,H5viewer); >>>> // Cleaning stage >>>> PetscViewerDestroy<http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Viewer/PetscViewerDestroy.html#PetscViewerDestroy> >>>> (&H5viewer); >>>> >>>> how can I add data that are just simple 1-D numbers stored on local >>>> arrays. >>>> Easier said, I would like to add the structured grid coordinates >>>> (first all x's, then all y's, and then all z's) at the end (or to the >>>> beginning) of each data (*.h5) file. But the grid coordinates are stored >>>> locally on each machine and not derived from any parallel vectors or DA. I >>>> was thinking about creating vectors and viewers using PETSC_COMM_SELF but i >>>> am not sure if that is the right approach since that vector is created on >>>> all processors locally. >>>> >>> >>> Use the DA coordinate mechanism and you can get the coordinates as a >>> parallel Vec. >>> >>> >>>> 2- When using VecView() and HDF5 writer, what is the status of data >>>> compression? >>>> The reason that I am asking is that, I used the same example above and >>>> comparing two files saved via two different PetscViewers, i.e. (just) >>>> Binary and HDF5 (Binary) the size is not reduced in the (*.h5) case. >>>> In fact, it is slightly bigger than pure binary file!! >>>> Is there any command we have to set in Petsc to tell HDF5 viewer to use >>>> data compression? >>>> >>> >>> We do not support it. We are happy to take patches that enable this. >>> >>> Thanks, >>> >>> Matt >>> >>> >>>> Thanks for your patience, >>>> Best, >>>> Mohamad >>>> >>>> >>>> >>>> >>>> >>> >>> >>> -- >>> What most experimenters take for granted before they begin their >>> experiments is infinitely more interesting than any results to which their >>> experiments lead. >>> -- Norbert Wiener >>> >> >> > > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://lists.mcs.anl.gov/pipermail/petsc-users/attachments/20120119/131beeb3/attachment-0001.htm>
